Microcystins - cyclic heptapeptide hepatoxins are produced by cyanobacteria most frequently belonging to the genera Microcystis, Anabaena, Nostoc and Oscillatoria. These algae are frequently found in eutrophic waters that are used for production of drinking water by artificial groundwater recharge. It is known that removal of MC-LR during transport though aquifer is a result of biodegradation [1], however there is concern that due to slow removal rate toxins will contaminate drinking water. The aim of this study - to determine removal efficacy of MC-LR during artificial groundwater recharge in aerobic and anaerobic conditions. For this the removal rate was studied in laboratory conditions and the obtained constants were used for the developing the mathematic modeling for removal MC-LR during artificial groundwater recharge in Riga, Latvia.